Koch Ina
Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany.
Mol Inform. 2010 Dec 17;29(12):838-43. doi: 10.1002/minf.201000086. Epub 2010 Nov 16.
In this review we introduce and discuss Petri nets - a mathematical formalism to describe and analyze chemical reaction networks. Petri nets were developed to describe concurrency in general systems. We find most applications to technical and financial systems, but since about twenty years also in systems biology to model biochemical systems. This review aims to give a short informal introduction to the basic formalism illustrated by a chemical example, and to discuss possible applications to the analysis of chemical reaction networks, including cheminformatics. We give a short overview about qualitative as well as quantitative modeling Petri net techniques useful in systems biology, summarizing the state-of-the-art in that field and providing the main literature references. Finally, we discuss advantages and limitations of Petri nets and give an outlook to further development.
在本综述中，我们介绍并讨论佩特里网——一种用于描述和分析化学反应网络的数学形式体系。佩特里网最初是为描述一般系统中的并发情况而开发的。我们发现它在技术和金融系统中有大量应用，但大约二十年来也被用于系统生物学中对生化系统进行建模。本综述旨在通过一个化学示例对基本形式体系进行简短的非正式介绍，并讨论其在化学反应网络分析（包括化学信息学）中的可能应用。我们简要概述了系统生物学中有用的定性和定量建模佩特里网技术，总结了该领域的最新进展并提供了主要文献参考。最后，我们讨论了佩特里网的优缺点，并对其进一步发展进行了展望。
